[Rtk-users] Blurred piece-wise reconstruction

[Chao Wu]

Ah, right, I see. itk::MemoryAllocationError.
So maybe less than 30 GB RAM is available at that moment...

Simon Rit <simon.rit at creatis.insa-lyon.fr> 于2020年2月13日周四 下午12:26写道：

> Well, the error was a CPU memory error, not a GPU error. But that should
> have fitted in RAM, I'm not sure why it didn't.
> On 2/12/20 1:20 PM, Chao Wu wrote:
>
> But streamerBP uses CPUOutputImageType so the 30Go is allocated on RAM
> instead of GRAM, so shouldn't be a problem...
>
> Regards, Chao
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> 于2020年2月12日周三 上午9:28写道：
>
>> Actually, the way I have implemented the streaming, it still allocates
>> the 30Go complete volume and compute it piece by piece. One thing you could
>> try is to remove the streamerBP object, connect directly the reconstruction
>> to the writer "writer->SetInput(pfeldkamp->GetOutput());" and set the
>> streaming in the writer
>> "writer->SetNumberOfStreamDivisions(args_info.divisions_arg);". Then it
>> never allocates the whole volume in memory. If that works for you, I think
>> you can open a PR on github with this change, that makes a lot more sense
>> in my opinion.
>>
>> On Tue, Feb 11, 2020 at 8:46 PM vincent <vl at xris.eu> wrote:
>>
>>> Hi Simon,
>>>
>>> yes, I used both in my command line.  I have 64 Go RAM on the machine,
>>> so that shouldn't be the issue.  For the sake of completeness, I also tried
>>> the subset option in combination with the divisions option, going as low as
>>> 1, but to no avail.
>>>
>>> I'll investigate further tomorrow.
>>>
>>> Thank you again for your help,
>>>
>>> Vincent
>>> On 2020-02-11 8:08 p.m., Simon Rit wrote:
>>>
>>> Have you tried the combination of both? To be clear, --divisions acts on
>>> the reconstructed volume so it should be ~7 Go with the "--divisions 4"
>>> option (instead of 2000*2000*2000*4/1024/1024/1024=29.8 Go otherwise).
>>> The --lowmem option acts on the projections and you have 250 Mo (instead
>>> of 2048*2048*1500*4/1024/1024/1024=23.4 Go otherwise).
>>> The message "Failed to allocate memory for image" seems to be a CPU
>>> memory issue. Are you sure you have about 10 Go available to run this
>>> reconstruction?
>>>
>>> On Tue, Feb 11, 2020 at 7:31 PM vincent <vl at xris.eu> wrote:
>>>
>>>> Hi Simon,
>>>>
>>>> I am afraid I forgot to mention something in my last email.  I tried to
>>>> use the lowmem option, as you suggested a while ago in the list for the
>>>> same problem, but I am afraid I am still getting the same error.
>>>>
>>>> kind regards,
>>>>
>>>> Vincent
>>>> On 11.02.20 17:36, Simon Rit wrote:
>>>>
>>>> Hi Vincent,
>>>> There is a way to do such a thing in rtkfdk with the --divisions
>>>> option, see code here
>>>> <https://github.com/SimonRit/RTK/blob/master/applications/rtkfdk/rtkfdk.cxx#L190-L196>.
>>>>
>>>> I also don't really understand either what's going on in your bottom
>>>> reconstruction, it seems to be a geometric problem. Have you checked an
>>>> axial slice?
>>>> Simon
>>>>
>>>> On Tue, Feb 11, 2020 at 4:21 PM vincent <vl at xris.eu> wrote:
>>>>
>>>>> Hello RTK community,
>>>>>
>>>>> I am afraid that my question might not be directly related to the
>>>>> excellent implementation we are all using, but it might still be
>>>>> interesting for some of you.
>>>>>
>>>>> I have a stack of 1500 projections of size 2048*2048.  I obviously
>>>>> can't
>>>>> reconstruct the full resolution volume on my graphics card, as it is
>>>>> too
>>>>> big.  So my solution was to split the sinogram into N parts, for which
>>>>> each reconstructed volume would fit in my GPU memory and then
>>>>> reassemble
>>>>> them.  I did a test with a 700*820*900 sinogram, that I cut in two
>>>>> parts
>>>>> of 700*410(+a small overlap)*900.
>>>>>
>>>>> While the reconstruction of the whole volume was acceptable, I got a
>>>>> weird issue with the split ones: the one corresponding to the top of
>>>>> the
>>>>> image is also ok, but the bottom one is very blurry.  The three images
>>>>> can be found at the following links:
>>>>>
>>>>> https://ibb.co/vLk9ZhQ
>>>>> https://ibb.co/m4pm0LT
>>>>> https://ibb.co/Jyf1yKM
>>>>>
>>>>> I used the same calibration parameters for the three reconstruction.
>>>>> I
>>>>> visually checked the split sinograms and they looked fine.
>>>>>
>>>>>
>>>>> Any insight will be much appreciated !
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> kindest regards,
>>>>>
>>>>> Vincent
>>>>>
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